Data
Normalization
Model options
Network processing
cor/cov method: pearson
Data
Normalization
See prepare.tcga.survival.data function for how to configure parameters.
This uses data packages from obtained from ‘github:averissimo/tcga’ that contain FPKM expression levels.
prepare.tcga.survival.data('kirc.data.2018.10.17',
'primary.solid.tumor',
normalization = 'center',
log2.pre.normalize = TRUE,
handle.duplicates = 'keep_first',
coding.genes = TRUE,
subtract.surv.column = '')
## [INFO] Loaded data from TCGA: kirc.data.2018.10.17
## [INFO] type of tissue: primary.solid.tumor
## [INFO] observations (individuals): 463 (151 event / 312 censored)
## [INFO] variables (genes): 19867
Network processing
cor/cov method: pearson
trans.fun is a double power to scale the valuessee ?glmSparseNet::heuristicScale or ?glmSparseNet::hubHeuristic
# see ?glmSparseNet::heuristic.scale
trans.fun <- function(x) {
heuristicScale(x) + 0.2
}
| ensembl_gene_id | degree | external_gene_name |
|---|---|---|
| ENSG00000150991 | 10394 | UBC |
| ENSG00000170325 | 6346 | PRDM10 |
| ENSG00000100300 | 5797 | TSPO |
| ENSG00000174775 | 5614 | HRAS |
| ENSG00000142208 | 5573 | AKT1 |
| ENSG00000111640 | 5363 | GAPDH |
| ENSG00000163631 | 5260 | ALB |
| ENSG00000177606 | 4952 | JUN |
| ENSG00000141510 | 4936 | TP53 |
| ENSG00000197122 | 4903 | SRC |
| ENSG00000254647 | 4592 | INS |
| ENSG00000112062 | 4187 | MAPK14 |
| ENSG00000170315 | 4114 | UBB |
| ENSG00000170345 | 4010 | FOS |
## [INFO] Size of sets: (size/events)
## * Train: 80.00% :: 369 / 120
## * Test: 20.00% :: 94 / 31
## [INFO] Number of variables per model:
| Model | BaseModel | Alpha | TargetVars | nvars |
|---|---|---|---|---|
| Elastic Net | Elastic Net | 0.20 | 69 | 69 |
| Hub | Elastic Net | 0.20 | 69 | 69 |
| Orphan | Elastic Net | 0.20 | 69 | 71 |
| Elastic Net | Hub | 0.10 | 41 | 42 |
| Hub | Hub | 0.10 | 41 | 43 |
| Orphan | Hub | 0.10 | 41 | 44 |
| Elastic Net | Orphan | 0.10 | 38 | 42 |
| Hub | Orphan | 0.10 | 38 | 38 |
| Orphan | Orphan | 0.10 | 38 | 39 |
## [INFO] note, selected variables could be slightly different from target, to have more accuracy increase nlambda in code
Calculated using the inferred models and the train/test datasets. The higher the better.
| weighted | penalization | project | tissue | cutoff | coding.genes | alpha | model | nvars | km.train | km.test | c.index.train | c.index.test |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| FALSE | string | kirc.data.2018.10.17 | primary.solid.tumor | 0 | TRUE | 0.20 | Elastic Net | 69 | 0 | 0.4800231 | 0.7989845 | 0.6002055 |
| FALSE | string | kirc.data.2018.10.17 | primary.solid.tumor | 0 | TRUE | 0.20 | Hub | 69 | 0 | 0.4312017 | 0.7874588 | 0.6264132 |
| FALSE | string | kirc.data.2018.10.17 | primary.solid.tumor | 0 | TRUE | 0.20 | Orphan | 71 | 0 | 0.3280982 | 0.7811956 | 0.5837616 |
| FALSE | string | kirc.data.2018.10.17 | primary.solid.tumor | 0 | TRUE | 0.10 | Elastic Net | 42 | 0 | 0.3995605 | 0.7425416 | 0.6192189 |
| FALSE | string | kirc.data.2018.10.17 | primary.solid.tumor | 0 | TRUE | 0.10 | Hub | 43 | 0 | 0.3531275 | 0.7465812 | 0.5858171 |
| FALSE | string | kirc.data.2018.10.17 | primary.solid.tumor | 0 | TRUE | 0.10 | Orphan | 44 | 0 | 0.6813939 | 0.7269392 | 0.5904419 |
| FALSE | string | kirc.data.2018.10.17 | primary.solid.tumor | 0 | TRUE | 0.10 | Elastic Net | 42 | 0 | 0.3995605 | 0.7425416 | 0.6192189 |
| FALSE | string | kirc.data.2018.10.17 | primary.solid.tumor | 0 | TRUE | 0.10 | Hub | 38 | 0 | 0.4517998 | 0.7417633 | 0.5781089 |
| FALSE | string | kirc.data.2018.10.17 | primary.solid.tumor | 0 | TRUE | 0.10 | Orphan | 39 | 0 | 0.9453068 | 0.7252715 | 0.5919836 |
(not running at the moment)
| metric | model | base.model | target.vars | alpha | mean | std | median | min |
|---|---|---|---|---|---|---|---|---|
| C-Index (Test set) | Hub | Elastic Net | 69 | 0.20 | 0.666 | 0.047 | 0.667 | 0.455 |
| C-Index (Test set) | Hub | Hub | 41 | 0.10 | 0.661 | 0.048 | 0.662 | 0.426 |
| C-Index (Test set) | Hub | Orphan | 38 | 0.10 | 0.660 | 0.048 | 0.661 | 0.427 |
| C-Index (Test set) | Elastic Net | Elastic Net | 69 | 0.20 | 0.687 | 0.045 | 0.688 | 0.501 |
| C-Index (Test set) | Elastic Net | Hub | 41 | 0.10 | 0.669 | 0.050 | 0.670 | 0.481 |
| C-Index (Test set) | Elastic Net | Orphan | 38 | 0.10 | 0.668 | 0.050 | 0.669 | 0.481 |
| C-Index (Test set) | Orphan | Elastic Net | 69 | 0.20 | 0.672 | 0.046 | 0.673 | 0.481 |
| C-Index (Test set) | Orphan | Hub | 41 | 0.10 | 0.659 | 0.050 | 0.661 | 0.45 |
| C-Index (Test set) | Orphan | Orphan | 38 | 0.10 | 0.658 | 0.051 | 0.659 | 0.445 |
| Log-rank (Test set) | Hub | Elastic Net | 69 | 0.20 | 0.044 | 0.103 | 0.007 | 2.57e-09 |
| Log-rank (Test set) | Hub | Hub | 41 | 0.10 | 0.061 | 0.122 | 0.013 | 4.23e-09 |
| Log-rank (Test set) | Hub | Orphan | 38 | 0.10 | 0.065 | 0.127 | 0.015 | 1.16e-08 |
| Log-rank (Test set) | Elastic Net | Elastic Net | 69 | 0.20 | 0.030 | 0.081 | 0.004 | 2.51e-09 |
| Log-rank (Test set) | Elastic Net | Hub | 41 | 0.10 | 0.059 | 0.127 | 0.011 | 1.36e-10 |
| Log-rank (Test set) | Elastic Net | Orphan | 38 | 0.10 | 0.060 | 0.128 | 0.012 | 1.36e-10 |
| Log-rank (Test set) | Orphan | Elastic Net | 69 | 0.20 | 0.046 | 0.103 | 0.008 | 5.88e-12 |
| Log-rank (Test set) | Orphan | Hub | 41 | 0.10 | 0.075 | 0.144 | 0.017 | 5.92e-09 |
| Log-rank (Test set) | Orphan | Orphan | 38 | 0.10 | 0.077 | 0.147 | 0.017 | 5.92e-09 |
| base.model | r.squared |
|---|---|
| Elastic Net with target nvars: 69 alpha: 0.20 | 0.6464047 |
| Hub with target nvars: 41 alpha: 0.10 | 0.6503503 |
| Orphan with target nvars: 38 alpha: 0.10 | 0.6376429 |
| base.model | r.squared |
|---|---|
| Elastic Net with target nvars: 69 alpha: 0.20 | 0.9177439 |
| Hub with target nvars: 41 alpha: 0.10 | 0.9428788 |
| Orphan with target nvars: 38 alpha: 0.10 | 0.9409778 |
| base.model | r.squared |
|---|---|
| Elastic Net with target nvars: 69 alpha: 0.20 | 0.6248941 |
| Hub with target nvars: 41 alpha: 0.10 | 0.6130614 |
| Orphan with target nvars: 38 alpha: 0.10 | 0.5999652 |
| metric | model | base.model | target.vars | alpha | mean | std | median | min |
|---|---|---|---|---|---|---|---|---|
| C-Index (Train set) | Hub | Elastic Net | 69 | 0.20 | 0.778 | 0.011 | 0.778 | 0.735 |
| C-Index (Train set) | Hub | Hub | 41 | 0.10 | 0.725 | 0.011 | 0.725 | 0.685 |
| C-Index (Train set) | Hub | Orphan | 38 | 0.10 | 0.721 | 0.011 | 0.721 | 0.683 |
| C-Index (Train set) | Elastic Net | Elastic Net | 69 | 0.20 | 0.780 | 0.011 | 0.780 | 0.74 |
| C-Index (Train set) | Elastic Net | Hub | 41 | 0.10 | 0.726 | 0.012 | 0.726 | 0.685 |
| C-Index (Train set) | Elastic Net | Orphan | 38 | 0.10 | 0.724 | 0.012 | 0.724 | 0.683 |
| C-Index (Train set) | Orphan | Elastic Net | 69 | 0.20 | 0.772 | 0.011 | 0.773 | 0.738 |
| C-Index (Train set) | Orphan | Hub | 41 | 0.10 | 0.717 | 0.011 | 0.717 | 0.673 |
| C-Index (Train set) | Orphan | Orphan | 38 | 0.10 | 0.715 | 0.012 | 0.715 | 0.67 |
| Log-rank (Train set) | Hub | Elastic Net | 69 | 0.20 | 0.000 | 0.000 | 0.000 | 0 |
| Log-rank (Train set) | Hub | Hub | 41 | 0.10 | 0.000 | 0.000 | 0.000 | 0 |
| Log-rank (Train set) | Hub | Orphan | 38 | 0.10 | 0.000 | 0.000 | 0.000 | 0 |
| Log-rank (Train set) | Elastic Net | Elastic Net | 69 | 0.20 | 0.000 | 0.000 | 0.000 | 0 |
| Log-rank (Train set) | Elastic Net | Hub | 41 | 0.10 | 0.000 | 0.000 | 0.000 | 0 |
| Log-rank (Train set) | Elastic Net | Orphan | 38 | 0.10 | 0.000 | 0.000 | 0.000 | 0 |
| Log-rank (Train set) | Orphan | Elastic Net | 69 | 0.20 | 0.000 | 0.000 | 0.000 | 0 |
| Log-rank (Train set) | Orphan | Hub | 41 | 0.10 | 0.000 | 0.000 | 0.000 | 0 |
| Log-rank (Train set) | Orphan | Orphan | 38 | 0.10 | 0.000 | 0.000 | 0.000 | 0 |
Distribution of Log-rank test with groups separated by high and low risk groups
Distribution of Log-rank test with groups separated by high and low risk groups
| base.model | r.squared |
|---|---|
| Elastic Net with target nvars: 69 alpha: 0.20 | 0.1939069 |
| Hub with target nvars: 41 alpha: 0.10 | 0.2725566 |
| Orphan with target nvars: 38 alpha: 0.10 | 0.2697257 |
| base.model | r.squared |
|---|---|
| Elastic Net with target nvars: 69 alpha: 0.20 | 0.4891016 |
| Hub with target nvars: 41 alpha: 0.10 | 0.6118420 |
| Orphan with target nvars: 38 alpha: 0.10 | 0.6275918 |
| base.model | r.squared |
|---|---|
| Elastic Net with target nvars: 69 alpha: 0.20 | 0.2155423 |
| Hub with target nvars: 41 alpha: 0.10 | 0.2623372 |
| Orphan with target nvars: 38 alpha: 0.10 | 0.2646656 |
i.e. with pvalue < 0.05 in Log-rank test using the test set.
i.e. with pvalue < 0.05 in Log-rank test using the test set.
| Gene | Overlap | total |
|---|---|---|
| ADM5 | 2 | 22238 |
| AR | 2 | 21690 |
| ADAMTS14 | 2 | 19458 |
| FBXL5 | 2 | 19110 |
| SORBS2 | 2 | 17563 |
| EME1 | 2 | 16070 |
| CDCA3 | 2 | 15211 |
| GPR173 | 2 | 14624 |
| IL4 | 2 | 13773 |
| CPLANE2 | 2 | 13405 |
| COL7A1 | 2 | 13322 |
| CCDC194 | 2 | 13237 |
| FAM72C | 2 | 12421 |
| KIF18B | 2 | 12225 |
| SLC5A6 | 2 | 11875 |
| IL6 | 2 | 11527 |
| UBC | 1 | 11214 |
| CDK2 | 1 | 11180 |
| ISG15 | 1 | 11138 |
| RHOA | 1 | 11101 |
ADM5(22238), AR(21690), ADAMTS14(19458), FBXL5(19110), SORBS2(17563), EME1(16070), CDCA3(15211), GPR173(14624), IL4(13773), CPLANE2(13405), COL7A1(13322), CCDC194(13237), FAM72C(12421), KIF18B(12225), SLC5A6(11875), IL6(11527), UBC(11214), CDK2(11180), ISG15(11138), RHOA(11101), SPANXB1(10996), UBB(10963), TROAP(10819), PLK1(10711), APCDD1L(10510), CDK3(10494), PRDM10(10380), TP53(10335), KDR(10224), ERFL(10166), HDAC1(10135), ONECUT2(9964), NCOA4(9743), CDK1(9631), LRRK2(9514), MBOAT7(9489), SEC61A2(9350), ZIC2(9326), CDK16(9153), BCL2(9067), TICRR(9054), GPR78(8853), TMEM150C(8790), EIF4EBP2(8730), CAD(8625), HES7(8584), CDC42(8584), SPATA18(8503), TSPO(8403), CPA5(8295), ANAPC7(8101), PABPC1L(8077), EMX2(7982), IFT20(7957), RIPK4(7938), JUN(7839), SLC16A12(7748), TRAIP(7711), TEDC2(7698), PTX3(7687), AC069503.2(7665), ATXN7L2(7652), CLTRN(7643), CRB3(7439), HES7(7434), SELENOP(7384), PIF1(7294), SRC(7229), METTL7A(7156), NFKB1(6973), RAC3(6900), ITGA8(6744), DLX4(6702), CCL7(6550), MYC(6464), MAPK3(6462), FAM72B(6425), DONSON(6282), HJURP(6267), POTEJ(6194), INS(6179), TLCD1(6022), SIGLEC6(5993), EPHB2(5919), KLRC2(5874), POTEI(5861), ACTC1(5754), AC138969.1(5728), NUMBL(5685), AMH(5645), SNHG28(5630), RHOBTB3(5547), GABBR1(5517), MXD3(5484), SAGE1(5403), REM2(5396), B3GNTL1(5348), STX1A(5339), C1orf94(5330), FAHD2A(5298), HSPA8(5273), AC008687.4(5210), CTNNB1(5201), SPANXC(5105), FAM20A(5059), PSRC1(4960), CKAP4(4719), ZNF117(4694), PANX2(4608), TPRG1L(4607), AC018630.4(4560), GBA3(4559), VAMP3(4511), PTPRB(4511), SAPCD1(4465), CAT(4312), COPS7B(4266), BARX1(4252), WDFY2(4250), SPRR2D(4147), DSCR9(4119), ASIC3(4096), CFAP45(4093), ACTA2(4093), C4orf3(4049), PTEN(3942), NUF2(3935), OR13A1(3901), NFKB1(3896), TBP(3887), LIMCH1(3876), POTEI(3863), FBF1(3845), C20orf141(3833), EPHB2(3832), CDRT15(3790), ERICH5(3750), AC092143.1(3733), RSKR(3725), POTEJ(3717), EMCN(3706), SRC(3698), CCR10(3696), RHNO1(3692), AKT1(3624), NCKAP5L(3623), GOLGA6L9(3557), PLPP3(3549), CCL7(3500), SLAMF9(3497), YARS1(3488), IGF1R(3483), RHOU(3483), AMOT(3465), HSPA8(3450), GGT2(3435), C9orf163(3434), PLXNB3(3432), CRABP2(3372), RAC3(3371), PYY2(3362), Z84492.2(3358), GART(3345), LRP8(3341), ACTB(3319), CCDC154(3271), KAT2A(3251), EP400P1(3236), CRPPA(3175), TMEM81(3146), RHOU(3135), YARS1(3105), PDGFD(3083), RHOB(3053), ITPKA(3040), RHOV(3039), CCL22(3012), MAGEA5(2996), RECQL4(2987), CALB2(2983), FLT3(2972), IGFL3(2960), MOCOS(2951), RAD51D(2933), TNF(2889), USP17L8(2884), LBX2(2878), RAC1(2827), ANKLE1(2770), ITGA6(2767), SARS2(2767), PRKAG3(2757), CHRNA9(2691), FOXM1(2686), SMIM24(2678), CYP3A7(2651), AC138969.1(2651), SPACA6(2641), MOB3B(2630), CSF3(2622), PYCR1(2620), SNF8(2593), ANHX(2572), PTPRB(2567), TTC32(2561), ALB(2555), RABL2A(2554), FAM209A(2547), ACTG2(2533), RSKR(2521), DMRTC1(2503), MAPK1(2493), RGS20(2492), C17orf50(2448), SLC18A3(2411), CNTNAP1(2395), AJAP1(2390), RAMP3(2388), MATK(2382), OBP2A(2378), TMEM138(2285), MMP24(2238), CAVIN2(2237), SLC40A1(2231), AKAP8L(2230), SORBS1(2227), KISS1(2206), SCX(2192), AGAP9(2189), HBP1(2188), FOSL1(2155), METTL24(2150), HS3ST3A1(2119), MGAM(2105), HRAS(2098), SLC7A5(2090), OTX1(2077), OTOF(2073), C6orf141(2056), KRTAP2-3(2056), ZSWIM2(2052), ACTL6B(2038), NFE4(2020), CENPBD1(1982), GAPDH(1955), JPT1(1954), TEK(1953), DBH(1937), STAT3(1915), FOS(1911), ACTBL2(1909), SLC2A9(1878), RHOB(1872), NRAS(1870), AL163636.1(1861), AC006254.1(1860), FGF17(1824), SSPOP(1818), GSDMB(1816), INAFM2(1812), MARS1(1799), SLC38A5(1795), KRTAP22-2(1768), TEX29(1766), NKAPD1(1750), PDE4D(1743), ANK3(1728), WFDC10B(1718), CDK5(1709), ZNF836(1651), UBE2S(1651), FAM53B(1648), INSR(1647), SOWAHB(1638), DENND4C(1623), CDKN1A(1618), SYCE1L(1616), CRP(1598), RHOQ(1579), LINC00313(1560), LINC02870(1542), HDAC9(1524), AL157935.2(1489), OSBPL1A(1489), IMPA2(1481), LILRA4(1479), GFPT2(1479), PTPRG(1476), ARMH1(1471), TOP2A(1466), EXOSC1(1448), FGF2(1441), KMT5A(1435), FLT3(1420), ST13(1416), CT45A8(1403), KPTN(1396), TMEM86B(1391), ADCY10(1383), RXFP1(1374), ZHX1-C8orf76(1372), UMPS(1369), MKRN3(1360), SPANXN1(1353), KLRC2(1342), CD1E(1321), UFSP2(1317), CERCAM(1309), GCK(1307), ATP6V1FNB(1306), FAU(1297), OAS2(1286), CDK6(1281), CORO6(1280), MAPK14(1268), LYRM7(1267), ASNS(1261), NPEPL1(1259), LRFN1(1258), RIT1(1244), SLC12A8(1206), DDX11(1185), KDELR3(1177), FRMPD2(1172), ABCC10(1158), ASNS(1137), SAPCD2(1124), SPIC(1119), MSTO1(1111), FOXL3(1108), RAP2A(1098), GPR162(1096), HACD1(1095), CDC7(1072), ATP8A1(1060), AURKB(1054), CDCA7(1044), OASL(1041), TNNT1(1027), PRKCG(1019), LYPD5(1012), STEAP1B(1008), FOXA2(991), PLIN4(989), KBTBD3(985), HNRNPCL4(980), PMF1-BGLAP(978), GNAO1(972), ATP2A1(967), PEX5L(955), GNB3(941), MAP6D1(941), F2(936), ZNF366(934), TPBGL(931), SGK1(926), HSP90AA1(924), MPV17L(919), CRADD(918), DMRTA1(916), CHCHD2P9(915), KRAS(915), GATA1(914), HSPA1L(912), POP5(907), GATA4(905), PINK1(900), DESI1(899), FCER1A(888), GIMAP6(884), GDF5(868), HOXA2(867), RAD51B(860), ZNF658(854), KRT79(839), KIAA1191(838), LPAL2(837), SP5(832), TUBB2A(829), CARS2(814), RBM3(812), KMT5A(808), GLI3(807), MLLT11(801), TRAPPC2B(793), RSPO4(790), HHLA2(786), MAGEA4(784), CA5B(780), UBL4B(779), EFCAB11(777), SPANXA1(768), C1QTNF8(760), STRADA(760), SCGB1C1(754), CD8B2(751), KBTBD11-OT1(736), COL21A1(735), CPXCR1(734), KRT39(734), RHEB(733), CHI3L2(730), CHTF18(729), MAPK12(725), C4orf19(724), KRTAP16-1(724), NPR3(720), CNTNAP1(719), SGK1(718), SLC10A2(712), KCTD16(710), TAFA3(710), RET(707), PDGFRB(702), STEAP3(700), TMEM158(695), MARS1(694), ITGA2(682), DEFB104A(681), TMEM200C(678), ULBP1(668), PLA2G2A(666), PTH(662), UTY(653), TNS1(648), AC079594.1(648), TPSB2(644), KLK11(639), RABL2B(638), RAP2B(637), SCN10A(632), FABP12(630), POFUT2(623), ESR1(618), FYN(616), ANKRD13D(612), PRKAR2B(609), RGS17(600), DIRAS2(598), NCR3LG1(597), AUP1(596), FBXL3(594), RHOQ(589), BCL6(586), TFAP2E(583), ADCY2(580), USP27X(567), FAM72D(564), ACTRT1(564), RNF41(558), SPEG(556), FBXO43(556), AKT3(549), PLPP5(546), GRIN3B(545), FEZF2(545), RPP40(538), ENGASE(538), EBLN1(536), EGFR(536), TSPY4(532), BIVM-ERCC5(531), HSPA1A(531), CNOT6L(530), ARHGEF37(529), CCDC166(529), C11orf45(526), BCL2L1(526), NBEA(524), LZIC(522), P2RY8(521), AC099811.2(516), PRKN(515), EPOP(511), MSH5-SAPCD1(511), FGFRL1(508), PCNA(507), RFLNA(505), ZNF583(503), SIX2(498), FOXP2(497), TMEM159(493), CILP(492), MAT1A(492), KRT75(488), TPSD1(486), RNF183(486), FLT1(479), AL035460.1(474), FOXL1(473), RAP2C(472), STK11(468), KCND1(466), ACTL9(466), FBXO48(464), SPATA31A1(460), SFN(459), AL121594.1(458), HDAC3(458), DCBLD2(452), PGPEP1(451), SERINC4(450), AC008758.6(449), TANGO6(447), MX2(446), RIN2(445), RGS20(444), RUNDC3B(441), MPP1(441), RGS17(440), MATN1(439), GIMAP6(437), ADIPOQ(434), A3GALT2(433), PDK4(433), AL163195.3(430), MELTF(429), CYYR1(428), FRMPD2B(427), MAP3K7(424), DRD5(419), GSG1(418), ERFE(417), ALDH3A2(414), TCEAL1(413), WNT5A(410), TTC32(410), OR4F5(410), IQGAP2(408), UCN2(406), FRMD5(399), NPIPB9(397), TCF7L2(395), ZNF658(394), CCER2(389), ACTRT2(387), MMP12(385), DNAAF6(383), SLC2A6(380), AC073610.2(379), DNAJC10(379), ELAVL1(376), MAGEC2(374), SCGB1C2(365), KLHL36(362), KRTAP4-16(362), GCK(362), SRCIN1(358), NIPAL3(352), KIAA1549(351), OR2B6(348), HDAC8(347), PECAM1(345), RHOBTB1(343), ZNF404(339), BBS4(338), MSH3(333), SYCE2(333), KCNIP2(329), RAVER2(329), CSF2(329), TMEM191C(328), UBL4A(328), KIF23(327), RERG(325), DNAJB1(324), SHISA9(324), GNL3(319), TTC1(317), XRCC3(317), IDUA(316), RNF13(315), TMCC3(313), PLIN1(313), CLDN4(313), GGT2(313), MYADML2(309), C2orf66(306), CTAGE8(304), OR10A6(304), RHOBTB2(302), AC036214.3(301), SLC12A8(301), FOSL1(299), DHRS3(298), CRACDL(295), ADH5(295), COL22A1(286), SLC25A37(285), CCNF(285), CPSF1(284), TDRD7(284), ABCB4(282), OTOF(282), ERBB3(281), CDK17(279), DUX4L9(276), OXT(274), STIMATE-MUSTN1(274), PTK6(273), TMEM132A(272), OR11H7(272), RERG(271), GOLGA8B(270), PRKAG1(268), OIT3(267), H3Y1(267), CDK15(265), FDCSP(261), GLI2(261), TIGD1(260), HOXA2(260), ZPLD1(259), NAT9(259), RNF19B(258), CPNE7(257), FAM227A(257), POTEE(257), FKBP9P1(256), COL22A1(251), PEDS1(250), ACTL8(248), EDNRB(248), IKBKE(248), MEP1A(247), EHMT1(247), PLA2G10(245), PRAMEF25(244), C4BPA(243), TMEM192(243), OAS1(241), SAA1(241), NUDT17(240), ZNF880(238), CHD1L(237), TSLP(236), IRX6(236), FUCA1(236), LRP5(234), PLS1(232), FKBP1C(231), BANF2(230), TAF10(230), FOXD3(229), RTEL1-TNFRSF6B(228), TMEM220(226), MAPK6(225), NAA40(224), CCDC189(223), RAB9A(218), ANKRD33(218), C9orf85(215), AC006486.1(215), F2RL3(214), CU639417.1(214), RANGAP1(213), VSX1(212), KLF6(212), AC005154.5(211), KALRN(211), SLU7(211), MAP7(210), CCDC85A(209), DGKK(209), FOXC1(207), COL20A1(206), CYP2C9(206), PEX6(204), AC009163.3(204), SLC2A6(204), BORCS7(203), KIAA1671(203), LTV1(202), PPP1R12B(201), MET(200), FGFR2(199), OR7A10(197), VNN3(196), THSD7B(195), RRAS2(195), BCL2L2-PABPN1(195), MYB(194), H2AX(193), SLC35E4(192), HMSD(190), UPK3B(188), TPBGL(187), CNTNAP5(186), REEP2(185), AC003688.1(185), ZNF521(185), JAK1(184), FAM218A(183), FGFR3(183), ERV3-1(181), KCNN4(181), CHRM3(181), CDY1(181), ACTR10(179), MRAS(179), UCN(179), ZIC5(178), NPIPA9(178), DECR1(178), PPP2R2C(177), CAMKV(176), NBR2(176), PLAC1(175), ZNF320(175), MYH14(175), USB1(173), PCDHGA9(172), SPTBN1(172), LRRC38(171), RXFP3(171), SPANXD(171), ERMN(171), ELN(170), LAMP5(170), CCNDBP1(170), LHB(169), TOMM34(168), RBIS(168), PCBP4(166), MAT1A(165), COQ7(164), SRCIN1(164), MDGA1(163), FAM174A(163), PPP1R3D(162), PCDHA11(162), MRGPRX2(160), AC091167.2(160), DUX4(159), AL109827.1(158), KRTAP13-1(157), RASD1(157), LSMEM1(155), MT1G(154), TXLNA(153), HSPA5(153), FAM166C(152), EHHADH(152), SLC3A1(152), NOP2(151), HACD1(151), C4orf33(149), ATOH8(149), GPAT2(149), UBE2D3(149), C10orf90(148), ABHD6(147), KIR2DL4(147), ZNF843(147), CTSG(145), ROBO3(145), CFAP298(144), PLEKHF2(144), OTOA(143), GATA3(142), C11orf58(141), FOXO6(141), ITGAE(141), RAPGEF4(141), ABCG2(140), MARCHF4(139), CHRD(139), ATP2A3(137), TRAPPC2(136), CYP21A2(136), IL23A(136), SFN(134), P2RY2(133), CMA1(133), SNF8(133), GNL3(133), PELI3(131), RUFY4(131), IGBP1P2(131), ENSG00000163009(131), OR7G1(130), NOS3(130), MYBL1(130), SEMA3A(129), HSPA4L(129), RND3(129), ZSWIM5(128), C1orf189(128), C16orf97(128), AC005702.1(128), C1RL(127), ROBO3(127), NPIPA1(127), CRLF2(127), TM4SF19-TCTEX1D2(127), PRICKLE4(127), ZFAND4(127), SGCB(126), RPS6KA1(126), UBD(126), ASCC1(125), HIPK4(124), MAGEH1(124), DENND1C(124), SAMM50(124), ASB16-AS1(123), RHBDF1(123), RORA(123), IGFLR1(122), LINC01620(122), CDK14(122), DMC1(121), TMEM47(120), RNF20(120), FAM160A1(120), ZNF879(119), RAD51(118), ITIH4(117), POLR3G(116), CFAP221(116), CCL8(115), AC244197.3(115), RAP1A(115), ACTA1(115), CRPPA(115), AC008878.3(114), AC091167.6(114), TPSG1(113), CST2(113), LINC00242(113), HSPA1L(112), SPRED3(111), AC009690.3(111), ZNF595(111), MT1F(110), C1orf53(110), DCLK1(110), OR10H2(110), PIMREG(109), JAK2(109), NPIPB6(108), KLHL9(107), CDK4(106), NAV3(105), ZNF304(105), LCK(105), DOCK8(104), TCTE3(104), EPB41L4A-AS1(104), FAM72A(104), GYG2(103), DFFA(103), SHOX2(103), PDGFRL(102), FGD5(102), TRPV3(102), PCSK5(102), SLC26A6(102), AC233992.2(101), AC244517.10(100), OGT(100), HGS(99), APOB(99), RPS6KB1(99), PURA(99), OSTN(98), RAPGEFL1(97), LRRC31(97), ELAPOR1(97), LINC00207(97), TTC6(97), COL4A5(97), C3orf35(97), LORICRIN(97), IZUMO4(96), RPS4Y2(96), FAM72A(95), LYPD8(95), ERAS(95), TRIM4(94), L1CAM(94), KAT14(94), ASB16-AS1(94), SCP2D1(91), IGFL2(91), CYP46A1(90), MMAA(90), THAP9(90), SOCS6(90), ARFGAP1(90), ALDH1A1(89), TTLL11(89), WFDC3(89), PISD(88), MOV10(88), BCL2L12(87), FOXD4L6(87), NPIPA1(87), HRH3(86), TF(86), ZNF420(86), LINC02868(85), PCDHGA12(85), MPZL2(84), ATG10(84), CXCL5(84), SNRPA1(84), SPANXN1(84), SLC52A2(82), CLMP(81), SRRM5(81), HEBP2(80), LINC02210-CRHR1(80), NHP2(80), EZHIP(80), ARL9(80), XG(79), TUBB2B(79), RPS27AP5(79), RAMACL(79), TMEM159(79), RPS6KA2(79), KCNN3(79), LBHD1(78), AGAP6(78), MTRNR2L6(78), NSUN5P1(77), TCTE3(77), TUBB3(76), POLR1D(76), CT45A9(76), MERTK(75), SLC25A37(75), LEP(75), FAM218A(75), PGRMC2(74), ACLY(74), WT1(74), NSUN5P1(74), TIRAP(73), KRT27(73), HNRNPCL1(73), EIF4B(73), IL2(73), AC093525.2(72), PDE6C(72), OGN(72), DDX41(72), ID2(71), XPO5(71), WBP1L(71), MROH2A(71), TTTY5(71), PDE6B(71), CHURC1-FNTB(70), IL31RA(70), RNF207(69), GTF2E2(69), MX1(69), CYP3A7(69), TOMM20(69), RNASE13(68), MAPK15(68), TMEM165(67), TOB2(67), PPIAL4C(67), DNAJA2(67), LIN54(67), LURAP1L(66), FASN(66), ATP8A1(66), MEF2B(66), DNAH8(65), THBS3(65), STIMATE-MUSTN1(65), C5AR2(64), RBM45(64), ABRAXAS1(64), SMARCA2(64), HSP90AB1(64), EGR1(64), ANKRD33B(63), SLC1A5(63), IFNG(63), FOXL2(63), SMIM29(63), RAB34(62), SLC26A10(62), SLC31A2(62), CDC20(62), ANXA8(61), TRMO(60), GALNT4(60), RASL10B(60), STEAP1B(60), PLCL2(60), PRKAR1B(60), COL11A1(59), CENPW(59), REM1(59), DHRS12(59), GARS1(59), UNC13A(59), CDADC1(58), ADAM8(58), TMEM191B(58), BCL3(58), SLX1A(57), DENND11(57), GTF2B(57), IFITM1(57), TMEM220(57), AC233992.2(57), CAPRIN2(56), PPP1R32(56), OTUD7A(56), CDK11A(56), ZNF543(56), SRRM5(55), FLRT3(55), PUS1(55), AC005154.5(55), SPATA4(54), AKAP6(54), EZHIP(54), EWSAT1(54), NBPF1(54), LY6G6D(54), HNRNPCL2(54), CCER2(54), RIBC2(53), CREBRF(53), LDLRAD4(53), SETSIP(53), C11orf54(53), ARHGEF28(53), CENPO(52), FOXP3(52), HESX1(52), TSPY1(52), NLRP10(51), AC003005.1(51), TBC1D8B(51), MITF(51), FAM53B(51), ZNF79(51), CXXC4(50), LINC01559(50), CCND1(50), PNPLA7(50), COPS4(50), NIM1K(50), BEX2(49), KIAA1614(49), AC011511.1(49), SEC24B(49), CEP83(49), U2AF1(48), FAHD1(48), QRFPR(48), CUBN(48), KCNAB1(48), POLDIP2(47), EREG(47), ALG3(47), SEC61A1(46), SCML2(46), SAMD1(46), SLC10A6(46), PALM2AKAP2(46), RBAK-RBAKDN(46), TGFB1(46), ITM2B(46), SOCS1(46), FAM13B(45), FAM47B(45), LINC02872(45), WNT3(44), PPP2CB(44), FOXA1(44), NSA2(44), RRAD(44), OR2V2(44), GTPBP2(43), MIIP(43), ABCC11(43), NUDT5(43), UBE2S(42), ASB17(42), STAG3L1(42), ALG1L2(42), CTSO(42), PAX6(42), RAB11A(42), DMGDH(42), HMGCLL1(42), C11orf45(42), AL157935.2(42), POLR2C(41), ZNF576(41), TMEM25(41), C21orf58(41), INAVA(41), GOLT1A(41), NPIPB5(41), CX3CL1(41), EPOR(41), LENG9(41), LMNB2(40), C3orf35(40), COL9A2(40), RHOJ(40), APOE(40), EPHB3(40), ENSG00000213865(39), ZBTB16(39), SHANK2(39), GAGE2A(39), MYO19(39), ORC6(39), AKT2(39), EIF4E3(39), C2orf76(39), TAAR6(38), AGBL2(38), ATF5(38), C10orf105(38), HP(38), URGCP-MRPS24(38), ACHE(38), TMEM245(38), DCST2(38), DSCR4(37), PCDHAC1(37), L34079.1(37), BUD23(37), LINC02872(37), SDR9C7(36), C4orf48(36), SMG9(36), RND2(36), RAD50(36), LDLRAD2(36), AC244197.3(36), CHAT(35), REPS2(35), KIR2DP1(35), KHDC1(35), MS4A2(35), CXCL8(35), CCDC137(35), TLR9(35), STRADA(35), MAST4(34), CFAP300(34), SHISAL1(34), CLDN25(34), HASPIN(34), BOP1(34), RCBTB2(33), MYBL2(33), SLC1A1(33), GEM(33), LONRF3(33), SOX12(33), MAGEA5(33), PRR23D2(33), TMEM135(32), FITM2(32), NPIPB2(32), AC008764.4(32), FAAP24(32), ERICH6B(32), DPAGT1(32), CCL24(31), ANO3(31), UGT2A3(31), NTPCR(31), IGFN1(31), H2BC18(31), PIK3CA(31), OR52I2(31), SMKR1(31), SVOP(30), SOCS3(30), LRRC73(30), TAFA5(30), SPINK8(30), H2BC8(30), LINC01138(30), DNM2(30), TSC22D1(30), SLC20A1(30), FARS2(30), CCDC74A(30), TTC24(30), TUBB7P(30), FOXP4(29), PRSS53(29), CCDC78(29), SERPINI1(29), BBS12(29), ZFP82(29), C2CD4B(29), CCT4(29), ADAM8(29), DIRAS3(29), CXCL1(29), TLN2(29), PRKAG1(29), DHRS7C(29), FAM50B(28), LRRC15(28), SNORC(28), AARSD1(28), REC8(28), C1orf159(28), GIPC2(28), EDA(28), SYNE3(28), EFNA5(28), TEAD4(28), CCNA1(27), LRRC37A3(27), RGS11(27), PTK6(27), KIF18A(27), PDZD2(27), EPHA10(27), EHMT2(27), LINC01089(27), LGALS2(26), STBD1(26), KRT2(26), PNMA8A(26), SPATA31D3(26), GPR33(26), PLPP5(26), PITPNC1(26), AKTIP(26), ADCY5(26), BACE2(26), RHPN2(25), GREB1L(25), CLDN14(25), VCX3A(25), KLLN(25), LIPA(25), CCNI(25), DNASE2B(25), EEF2(25), SLCO2A1(25), LPAL2(25), ACACA(25), CHAC1(24), CCDC81(24), SCFD2(24), ENSG00000269881(24), RTEL1-TNFRSF6B(24), WDR62(24), AMD1(24), CDKN1A(24), EGLN1(24), CARTPT(24), CCDC121(24), MTOR(24), SPACA7(23), GIMAP8(23), AC007731.4(23), CREBBP(23), SLC18A1(23), HDAC10(23), E2F5(23), CARS2(23), IGF2BP1(23), BORCS7(23), PBK(23), OR7D4(23), LINC01138(23), GGTLC3(23), COPZ2(22), RIPOR2(22), MASP1(22), KAAG1(22), MINAR1(22), TMEM270(22), SH2D7(22), CCDC137(22), CFAP73(22), TMEM233(22), GRIN2B(22), APLNR(22), DTX1(22), DCTN3(22), PHAX(22), SIX2(22), RHOD(22), NDUFAF8(22), GJA5(22), ARHGAP10(21), TOLLIP(21), NKAIN4(21), AVP(21), ZNF473(21), ADGRG3(21), ENO1(21), RASL12(21), JAK3(21), B3GAT1(21), TM4SF18(21), CCDC63(21), TRIB1(21), LSM1(21), PIDD1(21), FBXL6(21), RINL(21), ZNF542P(21), AC005726.1(21), FAM74A3(21), TXNDC15(20), GALNT12(20), ANGPTL8(20), NBPF3(20), KLF17(20), IL20RB(20), MT1M(20), DCDC2C(20), TMEM229A(20), GNAS(20), TIMP3(20), RGP1(20), NKX3-2(20), DBH(20), ASB8(20), C17orf107(20), OR8B4(20), FAM86C1P(19), ZFP64(19), HSD17B6(19), GSK3B(19), TTC28(19), ZNF821(19), TCIRG1(19), OIT3(19), USO1(19), NDUFS4(19), MAPK7(19), NPB(19), CTBP1-DT(19), KRTAP4-6(19), LILRA4(19), AL117348.2(19), MAPK8IP2(18), ILK(18), MANEAL(18), PPIAL4A(18), CD40LG(18), SPDEF(18), FOXF2(18), FBXL17(18), ABI3BP(18), SNORC(18), ZNF583(18), KRTAP16-1(18), ZNF812P(18), CNGA4(17), PRDM8(17), GPSM1(17), PWWP3A(17), LLCFC1(17), CTSF(17), SERF1B(17), RALA(17), STN1(17), MFSD1(17), HTR2C(17), PTPN9(17), DNAI2(17), OR51F2(17), CENPBD1(17), SMIM10L2A(17), PKP3(17), FAM200A(17), MGST2(16), LNX2(16), ASTN2(16), SPATA45(16), LINC02817(16), GIPR(16), RNF14(16), FOXN3(16), CARS1(16), REEP2(16), LBX1(16), MAPK13(16), CACNB3(16), ETV4(16), WFDC10B(16), DGAT1(16), CYP26C1(16), ANOS1(15), SLC17A9(15), B3GAT3(15), BTBD11(15), GNG3(15), ZFYVE19(15), WASHC1(15), CSAG3(15), COX15(15), CCDC85A(15), ATP11A(15), PCDH11Y(15), LGALS3BP(15), FARSB(15), TAF1L(15), RALB(15), SAP18(15), PTPRN2(15), LHX8(15), E2F7(15), ADORA2B(15), ZNF570(15), VPS37D(15), OPCML(15), TBC1D26(15), USP17L1(15), PPIAL4E(15), CYFIP1(15), AC091959.1(15), REC8(14), ZNF346(14), SENP8(14), DEFB124(14), SERPINB11(14), LINC01101(14), MYCBP2(14), GSC2(14), EED(14), TP53INP2(14), IL11(14), CSTF1(14), OAS3(14), SOD2(14), PEX5L(14), RAP1B(14), BLK(14), ANK2(14), POLE3(14), AGBL2(14), ZNF622(14), CLEC14A(14), NPEPL1(14), TMEM253(14), PHACTR3(13), BEX4(13), TMEM245(13), ART4(13), CSPG5(13), GH2(13), NARF(13), ARMC12(13), PGAP4(13), FAT3(13), MXRA7(13), AC008878.2(13), FGFR1(13), TUSC3(13), MT2A(13), BOLA3(13), ARHGAP42(13), TRMT61B(13), OR5B2(13), ROR1(13), SEMA3G(12), PRLH(12), CEMIP(12), DHDH(12), BST1(12), BCL11A(12), CPA4(12), PCDH8(12), DMRTA2(12), LGI4(12), VOPP1(12), PWWP3B(12), TRARG1(12), IPP(12), MUC21(12), CABP7(12), HIF1A(12), APEX1(12), CDS2(12), PGK1(12), GSG1(12), HHLA2(12), ALG5(12), RRP36(12), ZIC5(12), HSPG2(12), PAXX(12), ADPRHL1(12), ANKRD33B(12), PRKACG(12), CATSPER2(12), P2RY8(12), OLIG1(12), RPL23AP82(12), CCK(12), RTP5(12), DENND1C(12), PARP12(11), PIK3R1(11), LYSMD3(11), HPDL(11), MT1X(11), SBSN(11), KRTAP4-8(11), AL139300.1(11), AC090227.2(11), FAM136A(11), MEF2A(11), SIGLEC6(11), SLC12A7(11), RAPGEF5(11), PRKG2(11), TMEM47(11), RHPN1(11), SPRR2D(11), CRYL1(11), ANKRD33(11), NR0B1(11), CES2(11), OR52A4P(11), ANKRD34C(11), MKS1(10), CABP7(10), PLP1(10), GAL3ST2(10), C15orf48(10), SSX6P(10), MIR7-3HG(10), C1orf194(10), FOXD4L1(10), LIPI(10), DEFB115(10), SORBS1(10), DNAJC2(10), ACTR1B(10), CENPA(10), NFYB(10), PI3(10), ARHGEF16(10), ADCYAP1(10), GAREM1(10), ADPRH(10), SST(10), ATP2A2(10), ERFE(10), EDDM3B(10), CHEK2(10), SLC6A9(10), LINC01011(10), INAFM2(10), SMPD3(9), MLPH(9), PPP1R1A(9), PKIB(9), IL17RD(9), MXRA8(9), SSMEM1(9), KAT5(9), PLGLB1(9), NRN1L(9), KRTAP9-3(9), HLA-DQA2(9), AC018755.2(9), CACNG3(9), DMRT3(9), WNT3(9), KIF20A(9), CCNG1(9), PECR(9), CD207(9), PTGER2(9), KHDRBS3(9), IGF2BP3(9), CBX8(9), KIF2C(9), AQP10(9), DIP2C(9), CPT2(9), SHH(9), OR5I1(9), TUBB6(9), BNIP3(9), CYBC1(9), SYN3(9), TPSB2(9), OR6C3(9), ADGRG1(9), MMP12(9), ARL14EPL(9), CEACAM4(8), DKK1(8), TREM1(8), OSR1(8), OLAH(8), PID1(8), BPNT1(8), ART5(8), FBLL1(8), HLA-DQB2(8), LRRC37A2(8), ANK1(8), PRKACA(8), USB1(8), GRB10(8), EIF2B1(8), RNF19B(8), PROX1(8), HOXC11(8), SLPI(8), GSTM1(8), STK26(8), PSAT1(8), GCHFR(8), ACTR1A(8), TARBP2(8), ESD(8), ERBB2(8), SAMD1(8), SNCA(8), NOTCH1(8), FGF17(8), CCDC78(8), KCNK5(8), SENP8(8), PUSL1(8), S1PR1(8), ZNF404(8), ZBTB8OS(8), FKBP9P1(8), RIMKLA(8), APOLD1(8), MKRN3(8), SLC2A4(8), ODF3L1(8), SETD3(8), VSIG10L(8), EIF4EBP1(8), LCTL(8), CLDN4(8), ZNF836(8), L1CAM(8), FOXO6(8), AL354761.1(8), AC026954.2(8), AC005020.2(8), HIPK2(7), PCDHB15(7), EVA1A(7), CCDC91(7), PODXL(7), ATP8B3(7), TRIM43B(7), OTULINL(7), CCZ1B(7), ZC3H12C(7), FOXD4(7), HAS2(7), DENND2C(7), SLC25A22(7), SP140L(7), PRG2(7), LYPD6(7), TRNP1(7), RPS10-NUDT3(7), PRKCQ(7), TRIP13(7), TMEM38B(7), KLF5(7), PRX(7), CREB3(7), NEK2(7), ECRG4(7), KDSR(7), SPRYD7(7), PODXL(7), DAB2IP(7), PIM1(7), CFAP300(7), TM4SF19(7), FADS1(7), SKA1(7), KCNJ15(7), C1R(7), PGAP4(7), FRMPD2(7), PRKCE(7), GTPBP2(7), OR2T1(7), YES1(7), CLVS1(7), RPS6KA3(7), IFNL1(7), IQGAP3(7), C1QL4(7), SAXO2(7), NPIPB9(7), ZNF658B(7), CALM1(7), GPATCH3(7), R3HDM4(7), BTBD17(7), GIMAP1(7), LINC00115(7), CYP21A2(7), FAM90A20P(7), ZNF487(7), ABCA11P(7), ZNF723(7), DCP1A(7), H2AB1(7), SLC11A1(6), MAGEA10(6), MALL(6), MT1E(6), TRAPPC12(6), RBM20(6), RTL8B(6), PCDHGC5(6), CGB1(6), ENSG00000228439(6), PLPP1(6), GTSE1(6), AAAS(6), MSLN(6), MAP3K8(6), NEIL3(6), GLI1(6), PDE4D(6), ACTR8(6), ZFP30(6), TBC1D15(6), STX16(6), RPP40(6), NEDD8(6), HAUS8(6), CCNA1(6), RXFP2(6), KATNBL1(6), PPP3CA(6), HSPD1(6), ACTL7B(6), MMAA(6), RIT2(6), FAM81B(6), NPR2(6), GMPS(6), MSS51(6), HSP90B1(6), LINC00305(6), CYB5D1(6), F8(6), AJAP1(6), ZBTB12(6), ALG1L2(6), KBTBD11-OT1(6), BFAR(5), PYROXD1(5), BOD1(5), KCNJ15(5), CBS(5), CST1(5), TCP11L1(5), SLITRK2(5), FSCN2(5), S100A16(5), MMP1(5), H2AC19(5), TBC1D3(5), PPP5C(5), ZC3H3(5), PLEKHA5(5), NOA1(5), DNM1L(5), ZNF14(5), CPZ(5), MRPL18(5), RAB38(5), MYOD1(5), FKBP11(5), RAB33A(5), TRMO(5), SEMA7A(5), CARD14(5), ARHGEF19(5), UCK2(5), SNX30(5), CNBD2(5), RHBDL2(5), SHROOM4(5), OR3A3(5), ATAD3B(5), HELQ(5), CPA3(5), ZNF704(5), DDIAS(5), NPR1(5), KISS1(5), GIMAP8(5), XCR1(5), RUVBL1(5), CSTF3(5), BDNF(5), BASP1(5), LRRC37A3(5), SIX5(5), MAPK11(5), ZNF699(5), C20orf204(5), C1orf122(5), KPRP(5), ARSH(5), COLQ(5), LINC01588(5), SBK3(5), HGH1(5), AF241726.1(5), PPBPP1(5), AC007998.2(5), EPYC(4), CAPS(4), PRUNE2(4), WFIKKN1(4), POPDC3(4), RMDN3(4), CHODL(4), LALBA(4), GSDMA(4), DNASE1L2(4), BTD(4), GOLGA6L2(4), CD164L2(4), SCN4B(4), NPAP1(4), BCO2(4), SULT1C4(4), NSUN6(4), TNFSF12-TNFSF13(4), AC004691.2(4), TBXA2R(4), CELSR3(4), JADE2(4), HHAT(4), METTL22(4), ACTL6B(4), PHLPP1(4), ABL1(4), RASD2(4), CDKN3(4), SEL1L2(4), RP1(4), GSR(4), THEG(4), HAMP(4), DOCK8(4), FGF12(4), GUCY1B2(4), KCNS1(4), DTNA(4), AMHR2(4), NEK3(4), RHOF(4), ABL2(4), MEPCE(4), STK32B(4), C9orf85(4), CFAP161(4), KIT(4), PLA2G4D(4), CALHM4(4), TMEM135(4), NPIPB3(4), HSFY2(4), TRABD(4), UGT2B7(4), KLF17(4), UBQLNL(4), LMNB2(4), PFN4(4), OR2T8(4), HNRNPA0(4), GLIPR1L2(4), ZNF792(4), METTL23(4), LINC00471(4), ZNF329(4), ACTL10(4), NTM(4), TLCD2(4), NDOR1(4), ZBED6CL(4), HSH2D(4), ENTPD6(4), TUBA3C(4), RPS6KL1(4), SP5(4), TMEM191C(4), RNASEK(4), DUX4L9(4), SSU72P8(4), CCDC192(4), ZSCAN31(4), PABPC4L(4), SAA2-SAA4(4), AC092718.3(4), SPANXN2(4), COMMD3-BMI1(4), FAM25BP(4), DUSP14(4), OR6Q1(4), PPIAL4F(4), METTL22(3), ARHGAP4(3), TLL2(3), KIAA1549L(3), SLC25A23(3), EML2(3), DCST2(3), SLITRK5(3), SDHAF2(3), NCBP2L(3), C2CD4C(3), FAM110C(3), KRT5(3), RD3(3), MACO1(3), KRTAP3-2(3), LBH(3), ENSG00000213865(3), ENSG00000262621(3), CD9(3), CTNNA1(3), ANAPC4(3), GYG2(3), SNAP91(3), SMARCD1(3), PDK3(3), VPS35(3), SEMA3A(3), SLC46A1(3), TYRO3(3), EZR(3), CREM(3), NCR2(3), IZUMO4(3), HNF4A(3), SALL4(3), CDADC1(3), ACP5(3), RIPK2(3), FGF6(3), IL17A(3), PERP(3), TBX18(3), TBCCD1(3), MMP8(3), KLF9(3), MTERF2(3), KLHL7(3), TREM1(3), SRMS(3), FLNC(3), KNSTRN(3), LBP(3), PGPEP1(3), OLFM1(3), SHFL(3), ABCB7(3), LGR6(3), TTC9(3), C9orf40(3), WDR38(3), RHBDL3(3), BCL10(3), PRKACB(3), AFF3(3), CPXCR1(3), CLCA3P(3), GNA14(3), CD1E(3), CCDC24(3), C16orf86(3), GNE(3), GPSM1(3), RECQL4(3), DHRS3(3), IL31RA(3), ADCY1(3), AMOTL1(3), TEPSIN(3), VASN(3), GBX2(3), ASPSCR1(3), BTD(3), SP7(3), PPM1D(3), POLR1C(3), RXFP1(3), RND1(3), C1QTNF1(3), SUGCT(3), CCDC57(3), ACBD7(3), GAK(3), GJD3(3), FAM9A(3), KCTD16(3), CCR4(3), ACTG1(3), CRELD2(3), C1QTNF8(3), HSF1(3), SPATA31A6(3), CYP4F12(3), KRT10(3), FAM25A(3), FBXL22(3), AL662899.1(3), ZNF616(3), FBXO48(3), KRTAP5-6(3), TSGA13(3), PPM1N(3), SYCE3(3), PIGBOS1(3), DEFB130A(3), SPTY2D1OS(3), TRIM39-RPP21(3), AC069368.1(3), ZNF718(3), HOXA10(3), C1orf210(3), ALG11(3), CTSO(3), KLRA1P(3), AL355916.3(3), AC107871.1(3), AARSD1(3), AC090004.1(3), TEX28(3), MYO19(3), FP565260.6(3), AGK(2), GPRC5A(2), Z83844.1(2), MYLK2(2), C3orf14(2), PIGZ(2), ORMDL1(2), KLF4(2), CMTM7(2), TSPAN7(2), FBXO27(2), PYGO2(2), SYNPR(2), OTOP1(2), MZB1(2), TPSAB1(2), C2CD2L(2), GPR139(2), CFAP65(2), CIB1(2), TAL2(2), CCDC9B(2), LYPD2(2), C1orf174(2), FOXD4L5(2), LTC4S(2), PRAMEF11(2), AL672142.1(2), ZNF350(2), ZNF2(2), CCL18(2), ENSG00000281028(2), ENSG00000274897(2), MYLIP(2), GPRC5A(2), RETSAT(2), HERPUD1(2), PITX1(2), CHAT(2), SPAG5(2), ZNF416(2), PGS1(2), ASAP3(2), DNMT3B(2), MCOLN1(2), ZFHX4(2), COMT(2), PIM2(2), NDFIP2(2), HSDL1(2), SPAG1(2), SLC1A6(2), URI1(2), PDCD5(2), APLP1(2), MEIS3(2), IMPDH1(2), MEST(2), PSMD11(2), YWHAE(2), SH3D19(2), RAPGEF2(2), CREBL2(2), CD83(2), IL12B(2), PPP2CA(2), PRKAG3(2), IL1RL2(2), GADD45A(2), ARTN(2), HS1BP3(2), ELOVL3(2), RPL21(2), PRXL2A(2), EEF1E1(2), IL1B(2), GRIA3(2), UROD(2), RRAS(2), AUNIP(2), RIBC2(2), FEZF1(2), HOXD10(2), TRPM4(2), SLX1A(2), KMT5C(2), VRTN(2), KLHL36(2), TTLL4(2), EDAR(2), MMD2(2), POLR1E(2), KLC4(2), UQCC2(2), SMAD6(2), LNX2(2), TRIM65(2), SLC47A1(2), C1orf216(2), PFDN2(2), RORC(2), HHIPL2(2), NFKBIZ(2), TRIM4(2), NXF3(2), CETN2(2), FAM83A(2), NFIB(2), INIP(2), PAOX(2), SAA4(2), HMGA2(2), ADGRL3(2), HNMT(2), AKAP6(2), PTH(2), RETREG1(2), CNOT8(2), KCNMA1(2), TSPAN7(2), NSMCE2(2), PHKG2(2), GAREM2(2), KCNB1(2), CD1C(2), PAQR6(2), SPC24(2), TMEM82(2), SMCP(2), TRIM46(2), CCT3(2), CXCL5(2), H2AZ1(2), NUDT2(2), C1QL3(2), WDR72(2), YWHAB(2), DNAAF3(2), AC011511.1(2), BEST1(2), ATG4B(2), LINC01620(2), CXXC4(2), ATF5(2), OTUD7A(2), KLF13(2), CAVIN4(2), HTRA3(2), CYP4F22(2), HSFY1(2), NMNAT1(2), CD7(2), CNIH2(2), CABP4(2), LYSMD3(2), CALHM5(2), PRM3(2), PRR26(2), IGIP(2), MX2(2), ARSI(2), DNAH2(2), PRKX(2), A3GALT2(2), XPOT(2), UBE2G2(2), PRSS57(2), RGPD2(2), HGS(2), KRT79(2), ZNF829(2), CD300E(2), ACTL7A(2), KRTAP21-1(2), GPR21(2), IGFL3(2), PLEKHG4(2), ZXDA(2), ZNF568(2), C1orf53(2), MACO1(2), FKBPL(2), HSPA1B(2), MAS1L(2), PCDHA1(2), CRYGS(2), LTB4R(2), DENND10P1(2), TIGD1(2), UBA52(2), FAM30A(2), PRPS1L1(2), TSPAN19(2), CXorf51B(2), NME2(2), USP51(2), AC005324.3(2), EID1(2), MTRNR2L10(2), AL049844.1(2), POC1B-GALNT4(2), TGIF2-RAB5IF(2), CDC37P1(2), BOLA2-SMG1P6(2), SRSF8(2), GDF2(2), CSAG3(2), HEATR9(2), Z84492.1(2), AL024498.2(2), AC092587.1(2), USP27X(2), FP565260.1(2), C11orf98(2), HS3ST1(1), ZNF263(1), CYB561(1), SLC7A14(1), STMN4(1), GABRA1(1), NOP58(1), STYK1(1), DDX3Y(1), ATP2B3(1), HDAC4(1), TFRC(1), CD5L(1), PTGS2(1), NSF(1), TUBE1(1), RBM7(1), UBE2T(1), KCNN2(1), NDC80(1), CXCL2(1), CDC14B(1), ABCB1(1), CPNE3(1), GNAO1(1), IGBP1(1), PRTFDC1(1), RHBDD3(1), NEFH(1), LGMN(1), PYGB(1), SGK2(1), SLC17A9(1), CDC25B(1), TRIB3(1), CSNK2A1(1), PROKR2(1), HCK(1), PCSK1N(1), MAGT1(1), RGCC(1), N4BP1(1), ARL2BP(1), CCL22(1), EARS2(1), CPQ(1), FCGRT(1), IL4I1(1), HOXA1(1), HOXA3(1), PRKAG2(1), PRUNE2(1), AK1(1), GTPBP4(1), RECQL5(1), HLF(1), SULT1E1(1), PF4V1(1), INPP4B(1), HGFAC(1), LTA4H(1), LTBR(1), CMAS(1), BAG2(1), SEMA5A(1), FAM172A(1), GNPDA1(1), CHMP3(1), PASK(1), PIK3R3(1), HSD11B1(1), RPA2(1), HMGN3(1), ZC2HC1C(1), TCTN3(1), SFRP5(1), TNN(1), IQSEC3(1), KBTBD7(1), LIAS(1), RASL11A(1), HS3ST2(1), FAM124B(1), MC3R(1), FAM210B(1), KCNK17(1), NRN1(1), RAB17(1), CXCL6(1), GPR108(1), TNFSF14(1), L3HYPDH(1), MASP1(1), TUBA4A(1), ORMDL1(1), CALML4(1), EPB41L4A(1), NCAN(1), MNX1(1), MED18(1), KREMEN2(1), CDK8(1), C1QTNF6(1), ACTR3B(1), GSC(1), CATSPERB(1), PLEKHA8P1(1), SAA2(1), ANO3(1), KCP(1), TEC(1), MDM2(1), RCBTB2(1), ZDHHC4(1), CALCOCO2(1), CDK9(1), ARPC5L(1), TLR2(1), C11orf1(1), MMP13(1), HERC3(1), C1RL(1), ESR2(1), SCAPER(1), SPATA22(1), WNT9A(1), PHLDB2(1), PLA2G7(1), TMEM140(1), FAM135B(1), HMCN2(1), CNNM2(1), B3GAT3(1), GPHA2(1), LYPD1(1), DIXDC1(1), PRSS53(1), ANO4(1), INPP1(1), PABPC3(1), PELO(1), CLGN(1), PTPRR(1), CD8A(1), SPHKAP(1), CYP2U1(1), C2CD6(1), MPV17L(1), FCHO2(1), CNOT11(1), ABCG1(1), DVL3(1), TNFSF13(1), PPP1R32(1), TSSK3(1), NFIA(1), SNX7(1), C1orf74(1), ZSWIM2(1), TCF23(1), SMIM12(1), RHO(1), METAP1(1), HPGD(1), HHIP(1), F2RL1(1), CSF2(1), CREBRF(1), EN2(1), MICALL2(1), YWHAZ(1), NLGN4Y(1), STK32C(1), PTER(1), ADAMTS15(1), TK2(1), TMEM170A(1), JSRP1(1), ZNF526(1), TBX10(1), OR1F1(1), GNG4(1), TNIP2(1), GCSAML(1), CA5B(1), BCRP2(1), CALML6(1), NPAS2(1), SOCS6(1), TPD52L3(1), KRT13(1), ZNF561(1), OR8J1(1), CBWD1(1), ANKRD13D(1), RELA(1), DELEC1(1), AC097637.1(1), FAM166C(1), LRFN4(1), RGMB(1), C12orf76(1), B4GAT1(1), SLC66A1L(1), OR5J2(1), FOXR1(1), ZSCAN2(1), GNG7(1), CNTD1(1), LY6H(1), MTHFR(1), FAM210A(1), OR2M7(1), SLC25A22(1), IMPDH2(1), GEN1(1), RNF186(1), FBXO34(1), C3orf38(1), CCDC89(1), PLD6(1), DCTPP1(1), C3orf80(1), MIGA1(1), MB21D2(1), ZFP3(1), OR56B4(1), GPR62(1), TCEAL8(1), NPM1(1), WASHC1(1), P2RY13(1), MCEMP1(1), TREX2(1), DGCR6(1), GPR1(1), IQCF2(1), ACTRT3(1), LRRC19(1), ZFP1(1), C6orf58(1), H2BC21(1), DRD1(1), DMRTC1B(1), RAB11B(1), SHC4(1), POU3F1(1), ARL17A(1), TMEM210(1), NAP1L2(1), C17orf58(1), OR10H1(1), TRABD2A(1), PCDHB13(1), SBK2(1), NHEJ1(1), ARL4C(1), DUSP21(1), CGB5(1), DCAF8L2(1), FAT4(1), CTSE(1), WDR5(1), HDAC2(1), DYNC1H1(1), KCNMB2(1), SCGB1D4(1), UGT2B17(1), SULT1C4(1), ZNF813(1), ZXDB(1), SH3BGRL2(1), ANKRD13B(1), OR10Z1(1), RAET1G(1), RPL12P1(1), PJVK(1), SKIV2L(1), TRIM13(1), TMEM240(1), TMEM88B(1), C11orf91(1), LGR4(1), KRT6A(1), MANSC4(1), CYS1(1), CSNK1E(1), AMZ2P1(1), IQCF6(1), C12orf71(1), MTCP1(1), CXorf49(1), TENM3(1), UMAD1(1), ZNF826P(1), TWIST2(1), LINC02817(1), HNRNPUL2-BSCL2(1), FAM237A(1), SPAAR(1), LINC01554(1), TMEFF1(1), TUNAR(1), TMED7-TICAM2(1), FOXD1(1), INMT-MINDY4(1), PCDHA3(1), LY6G6E(1), PRECSIT(1), SMIM10L1(1), MTRNR2L1(1), KLRF2(1), RPL36A-HNRNPH2(1), AL136295.3(1), AC138894.1(1), OR1D5(1), RBM8A(1), AC004805.1(1), LINC01140(1), GABRQ(1), AC010326.2(1), ERVV-1(1), BIVM-ERCC5(1), MTRNR2L11(1), MROH7-TTC4(1), RBAK-RBAKDN(1), CCL3L3(1), DHRS11(1), GIMAP1-GIMAP5(1)
[INFO] Coefs. list
[1] “ABCB4, AC008687.4, AC008758.6, ADM5, AJAP1, AL035460.1, AMH, ANAPC7, APCDD1L, AR, ASIC3, ATP8A1, BANF2, CCDC194, CCL22, CCL7, CCR10, CDCA7, CDRT15, CFAP45, CNTNAP1, COPS7B, CRP, CYP3A7, DEFB104A, DMRTC1, DNAAF6, DPAGT1, DRD5, EME1, ERFL, FAHD2A, FAM20A, FAM53B, FBXL5, FGF17, GPAT2, GPR78, HES7, HNRNPCL4, IL4, KBTBD11-OT1, KISS1, KLRC2, MAGEA5, MELTF, MKRN3, MPV17L, ONECUT2, OR8B4, OTX1, PABPC1L, PTX3, RHNO1, RNF183, SAGE1, SEC61A2, SERINC4, SIGLEC6, SLC18A3, SLC5A6, SLC7A5, SNF8, SNHG28, SORBS1, SPANXB1, SPATA18, SPRR2D, STRADA, USP17L8, VAMP3, Z84492.2, ZNF880”
[INFO] Coefs. list
[1] “AC099811.2, ACTA2, ACTC1, ACTG2, ADIPOQ, ALB, ANK3, AR, ATP2A1, CDC42, CDK2, CDK3, CDK6, CPLANE2, CSF3, DIRAS2, EFCAB11, EPHB2, FGFRL1, FOXP2, GGT2, GNAO1, HDAC1, HSPA8, IGF1R, IL4, IL6, INS, ISG15, JAK1, JUN, KAT2A, KDR, KMT5A, KRAS, MATK, MYC, NFKB1, NRAS, OAS2, PDE4D, PLK1, POTEI, POTEJ, PRDM10, PRKAG3, PRKCG, PTH, RABL2A, RAC3, RAP2A, RHOA, RHOB, RHOBTB3, RHOQ, RHOU, RHOV, RIPK4, RSKR, RXFP1, SFN, SGK1, SMARCA2, SRC, STAT3, TNF, TP53, UBB, UBC”
[INFO] Coefs. list
[1] “AC008687.4, AC069503.2, AC138969.1, ADM5, ANHX, APCDD1L, AUP1, BORCS7, C16orf97, C1orf53, C20orf141, C2orf66, C4orf19, C4orf3, C9orf163, CCDC166, CCDC194, CCR10, CENPBD1, CFAP45, CKAP4, CLTRN, CPXCR1, CT45A8, DMRTC1, DSCR9, EMX2, ERICH5, ERV3-1, FAM72B, FAM72C, FBXL5, GOLGA6L9, GPR78, HES7, HS3ST3A1, IFT20, INAFM2, ITGA8, LIMCH1, LINC00313, LINC02870, MAGEA5, MMP24, NCOA4, ONECUT2, POLR3G, PTX3, RHNO1, RNF183, SAPCD1, SCGB1C2, SETSIP, SIGLEC6, SLC5A6, SMIM24, SNF8, SNHG28, SORBS1, SORBS2, SPANXB1, SPATA18, TEX29, TLCD1, TMEM200C, TMEM233, TMEM81, TPBGL, VRTN”
[INFO] Coefs. list
[1] “AC138969.1, ADM5, AMOT, ANAPC7, AR, AUP1, B3GNTL1, CCL7, CDCA3, CLTRN, CNTNAP1, COL7A1, CRABP2, EIF4EBP2, EMX2, FBXL5, GPR173, HES7, IL4, IMPA2, ITGA8, LRFN1, METTL7A, MSH5-SAPCD1, NUF2, OTX1, PABPC1L, PIF1, PTX3, SAMM50, SEC61A2, SLC16A12, SLC2A6, SLC5A6, SLC7A5, SNF8, SORBS2, SPATA18, TRAIP, ZIC2, ZNF117”
[INFO] Coefs. list
[1] “AC092143.1, ACTA2, ACTC1, ACTRT1, ALB, AR, BCL2, CAD, CALB2, CCL7, CDC42, CDK1, CDK16, CDK17, CDK2, CDK5, CDKN1A, CPLANE2, EPHB2, FGF2, FGFR3, FOSL1, GGT2, HDAC1, HSPA4L, HSPA8, IL4, IL6, ILK, INS, ISG15, JUN, KDR, KMT5A, KRAS, LRRK2, MATK, MGAM, MYC, NFKB1, PDE4D, PLK1, POTEI, POTEJ, PRDM10, PRKAG1, PRKAR2B, PTEN, PTH, RAC1, RAC3, REM2, RHOA, RHOBTB3, RHOU, RHOV, RIPK4, RSKR, SEC61A2, SRC, TNNT1, TOMM34, TP53, TTC32, TUBB2A, UBB, UBC, WDFY2, YARS1”
[INFO] Coefs. list
[1] “AC008687.4, AC069503.2, AC138969.1, ADM5, ANHX, APCDD1L, AUP1, BORCS7, C16orf97, C1orf53, C20orf141, C2orf66, C4orf19, C4orf3, C9orf163, CCDC166, CCDC194, CCR10, CENPBD1, CFAP45, CKAP4, CLTRN, CPXCR1, CT45A8, DMRTC1, DSCR9, EMX2, ERICH5, ERV3-1, FAM72B, FAM72C, FBXL5, GOLGA6L9, GPR78, HES7, HS3ST3A1, IFT20, INAFM2, ITGA8, LIMCH1, LINC00313, LINC02870, MAGEA5, MMP24, NCOA4, ONECUT2, POLR3G, PTX3, RHNO1, RNF183, SAPCD1, SCGB1C2, SETSIP, SIGLEC6, SLC5A6, SMIM24, SNF8, SNHG28, SORBS1, SORBS2, SPANXB1, SPATA18, TEX29, TLCD1, TMEM200C, TMEM233, TMEM81, TPBGL, VRTN”
NULL
## [INFO] balanced.sets: TRUE
## [INFO] calc.params.old: FALSE
## [INFO] coding.genes: TRUE
## [INFO] degree.correlation: pearson
## [INFO] degree.cutoff: 0.000
## [INFO] degree.type: string
## [INFO] degree.unweighted: TRUE
## [INFO] handle.duplicates: keep_first
## [INFO] log2: TRUE
## [INFO] n.cores: 14.000
## [INFO] normalization: center
## [INFO] ntimes: 5000.000
## [INFO] project: kirc.data.2018.10.17
## [INFO] seed: 1985.000
## [INFO] subset: Inf
## [INFO] subtract.surv.column: (I do not know how to display this)
## [INFO] target.vars: list(alpha = 0.2, vars = 69), list(alpha = 0.1, vars = 41), list(alpha = 0.1, vars = 38)
## [INFO] tissue: primary.solid.tumor
## [INFO] train: 0.800